AtomicSystem.add_atoms

AtomicSystem.add_atoms(atypes, positions, charges=None, masses=None)

Add multiple atoms to the system in a single operation.

Parameters:

atypeslist of str or int, or np.ndarray

Atom types (e.g. ['H', 'Ow', 'Ca']).

positionsarray-like of shape (n, 3)

Cartesian coordinates in Angstroms.

chargesarray-like of shape (n,), optional

Partial charges in elementary charge units. Default is 0.0 for each atom.

masseslist of float, optional

Atomic masses in g/mol. If None, masses are looked up in MASSES_DICT or default to 1.0 for unknown types.